Genomics
Genomics encompasses extraction, genotyping, sequencing and other genomics-related services across a range of UQ facilities.
Services
- DNA extraction
- Quantitative PCR
- Amplicon sequencing and community profiling
- Metagenomics
- Metatranscriptomics and RNA sequencing
- Single Cell Genome Analysis
- Oxford Nanopore long read sequencing
- Microbial bioinformatics
Equipment
- Illumina
- Illumina MiSeq
- Oxford Nanopore MinION
- Oxford Nanopore PromethION
Contact
Sequencing Manager
Website: School of Chemistry and Molecular Biosciences
Phone: 07 3365 4318
Email: ace_sequencing@uq.edu.au
Location: St Lucia campus
Services
The Australian Genome Research Facility (AGRF) is a key enabler of world-class genomic science and offers a range of services covering all aspects of genomics. Services include:
- Next Generation Sequencing
- Microbial Diversity Profiling
- Genotyping
- Genetic ID
- Long Read Sequencing
- Sanger Sequencing
- Gene Expression
- Bioinformatics
- Nucleic Acid Extraction
Equipment
- Illumina NovaSeq X
- Illumina NextSeq 2000
- Illumina MiSeq
- PacBio Revio I
- Agena MassArray
- Illumina iScan
Contact
Website: Australian Genome Research Facility
Phone: +61 3 9321 3700 or Freecall 1300 247 301
Email: CustomerCare@agrf.org.au
Location: St Lucia campus
Services
The Australian Genome Research Facility (AGRF) and UQ collaborate as a joint Certified Service Provider (CSP) providing Long Read Sequencing using the PacBio Sequel II. The AGRF-UQ PacBio Service expands their capabilities in long-read PacBio® sequencing for generating high-quality genome assemblies, comprehensive transcriptome analyses, and epigenetic information.
As a Certified Service Provider for Single Molecule, Real-Time (SMRT®) Sequencing, this collaboration offers the Sequel II System for affordable, high-throughput studies of microbes, plants and animals, or humans.
Equipment
- PacBio Sequel II
Contact
Dr David Hawkes
Website: AGRF-UQ PacBio Service
Phone: 07 3346 9682
Email: david.hawkes@agrf.org.au
Location: St Lucia campus
Genetic Research Services (GRS) provide high-quality genetics services to both UQ and external clients. Backed by a multi-disciplinary team and state-of-the-art equipment, we offer a number of services to support your research needs.
Services
- Rodent genotyping service – We genotype all types of genetic modifications including knockouts, knockins, conditional/floxed, transgenes, SNPs, and CRISPR. The service includes genotyping assay design, DNA extraction, and fluorescent PCR coupled with capillary electrophoresis for highly accurate and sensitive detection of assay products. The genotyping results are analysed by a team of highly experienced research staff.
- Sequencing – We offer high quality, fast, customised services for sequencing clients. We also provide customised solutions and specialised customer support for troubleshooting undesirable results and offer different sequencing dyes (v3.1 and v1.1) for particularly difficult DNA templated eg. hairpin or highly repetitive regions. The Sanger DNA sequencing service is performed on our two 3730 Applied Biosystems capillary electrophoresis machines.
- Fragment services – Our fragment analysis service can speed up your research by analysing your PCR results in a 96-well plate format using high-throughput CE DNA analysers. Fluorescently labelled PCR products from 50-1100 base pairs can be analysed and differences in fragment size as little as 1 base pair can be detected. PCR assays are commonly used to screen for the presence or absence of a variety of genetic features, e.g. insertions, deletions, and SNPs, in a range of organisms.
- Robotics services – We have a number of automated robotic instruments for laboratory work (pre and post PCR), PCR machines and 3730 DNA analysers that may assist you with your high throughput laboratory needs. PCR automation and automated processing reduces the risks of injury, errors, and time associated with the manual processing of high numbers of samples within the laboratory. We can help with automating DNA extraction, PCR, and PCR set up and plate preparation.
- Microsatellite/STR panels – We can optimise microsatellite panels, perform capillary separation, and analyse the results for a variety of animals including, but not limited to, horses, sharks, and manta rays.
- Bacterial 16S testing – Our bacterial 16S test detects the presence of the 16S ribosomal subunit gene which is highly conserved in the genomes of many different strains of bacteria. This test can be useful for applications such as detection of bacterial contamination in faecal samples from germ-free mice in gnotobiotic facilities and for monitoring of sterile environments. Positive 16S results can also be investigated to try and identify the bacterial strain via further 16S sequencing and comparison to online databases.
Contact
Ms Leanne Clarke
Manager
Website: Genetic Research Services
Phone: 07 3365 3647
Email: uqgrs@uq.edu.au
Location: St Lucia campus
Genome Innovation Hub (GIH) is a UQ initiative and is part of UQ Research Infrastructure. GIH aims to develop innovative approaches to advance technologies in structural and functional analysis of genomes. The innovation hub acts as a collaborative research centre, working with UQ clinicians and scientists to implement novel and promising methodologies in projects focussed on the key areas of health, agriculture and the environment.
Services
- Single-cell sequencing and library preparation
- Long read sequencing
- Protein engineering and purification
- Genome editing and manipulation
- Spatial transcriptomics and advanced imaging
- Bioinformatic assembly of complex genomes
- Transcriptomics
- High throughput genetic screening platforms
- Computational tool development for analysis of genomic and transcriptomic data
- DNA and RNA extraction from difficult sources
- Microfluidic partitioning and barcoding for single-cell analysis
Contact
Stacey Anderson
Operations Manager
Website: Genome Innovation Hub
Phone: 07 3346 2077
Email: s.andersen2@uq.edu.au
Location: St Lucia campus
Services
Standard library preparation and sequencing services include:
- Illumina (short read) whole transcriptome sequencing for gene expression profiling or deeper transcriptome analysis
- 10x Genomics Chromium Single Cell 3' Gene Expression (including CITE-seq/cell hashing)
- PacBiowhole genome sequencing (long reads and HiFi reads)
- PacBio IsoSeq (full length transcript analysis)
In addition, we are happy to discuss how we can help with your custom sequencing requirements. We have experience with library prep and/or sequencing in the following areas:
- Exome and custom capture
- Illumina sequencing panel
- Amplicon sequencing
- Sequencing customer-prepared libraries
- 10x Genomics Chromium VDJ and Single Cell ATAC assays
- Spatial transcriptomics
- ATAC-seq
- CAGE
- Small RNA
- Hi-C
RNA and DNA quality control:
- Agilent Bioanalyser
- LabChip GX Touch
- Invitrogen Qubit
Equipment
- Illumina NextSeq 500 platform
- Illumina MiSeq platform
- 10X Genomics Chromium Single Cell system
- PacBio Sequel II
Contact
Angelika Christ, Dr Tim Bruxner or Shivangi Wani
Website: Institute for Molecular Biosciences
Phone: 07 3346 2074
Email: seq-core@imb.uq.edu.au
Location: St Lucia campus
Services
Cell and animal model CRISPR genome editing:
- gene knock-out
- large fragment deletion
- knock-in (SNP, reporter, floxp, etc.).
Cell line engineering - Generation of stable expression cell lines using:
- safe harbour locus CRISPR knock-in
- Piggybac transposon system.
Lentiviral particle production:
- high titers of ≥ 108 TU/ml (transducing unit per ml) – only for UQ-wide community.
Other cell line service:
- CRISPR and Transfection optimisation
- karyotyping
- mycoplasma testing
- genotyping and CRISPR analysis.
Equipment
- Neon electroporation system – Thermo Fisher Scientific Neon
- 4D Nucleofector System – Lonza (shared by Genome Innovation Hub)
- Countess II FL Automated Cell Counter – Thermo Fisher Scientific (shared by Genome Innovation Hub)
Contact
Dr Xiaoli Chen
Website: CRISPR Services
Phone: 07 3346 2348
Email: qfage@imb.uq.edu.au
Location: St Lucia campus
Services
Quantitative 'real time' PCR (qPCR) instruments measure the accumulation of signal generated by fluorescent dyes during each cycle of PCR. SCMB qPCR facility offers a range of instrumentation for qPCR set up, data acquisition and data analysis. We provide training, instruments, lab ware, SYBR reagent and working space, just bring your samples.
Equipment
- AB-QuanStudio 6 qPCR machine: 6-colours (green to far-red), 384-well plate block, QantStudio software. SYBR and TaqMan compatible.
- AB-Viia7 qPCR machine: 6-colours (green to far-red), 384-well plate block, QantStudio software. SYBR and TaqMan compatible.
- QIAGEN –Rotor-Gene-Q qPCR machine: 72-tubes rotor, 2 colours (green 470Em/510Em and yellow - 530Ex/557Em)
- Eppendorf epMotion 5075/5073 pipetting robotics system
- Integra AssistPlus pipetting robot with Viafo and Voyager electronic 8- or 12- channel pipettes
- Laminar-flow hood, multichannel pipets and plastic ware for manual PCR stet up
- Maxwell16 DNA/RNA/Protein isolation robot
- QBIT-4 fluorometer for fast and sensitive quantification of DNA, RNA, and Protein
Contact
Dr Vitaliya Sagulenko
Website: School of Chemistry and Molecular Biosciences
Phone: 07 3346 7539 or 0409 132 834
Email: v.sagulenko@uq.edu.au
Location: St Lucia campus